41.9% of periodontitis in the USA is attributable to smoking, and smokers are at a higher risk for more severe and extensive disease than non-smokers. Although both bacterial plaque and smoking are reported to play important roles in periodontitis, associations between individual bacterial species or consortia and smoking have not been well elucidated. Recent cultivation-independent explorations of the subgingival microbial community have revealed that the majority of species are uncultivated and hence, unrecognized when using traditional, cultivation-based approaches. Therefore, it is important to examine the subgingival microbial profile of this high-risk population using molecular approaches that circumvent the need for cultivation. We hypothesize that smoking is associated with an alteration in the subgingival microbial profile and that this alteration is independent of disease severity. We propose to use bead-probes directed to the 16S rRNA genes to simultaneously measure the levels of multiple species with a flow cytometer. Specific aim 1 proposes to investigate if smoking is associated with a global perturbation of the subgingival ecosystem by comparing levels of cultivated species and as-yet-uncultivated phylotypes between periodontally healthy smokers and those with periodontitis. These species have been selected based on our earlier work using an open-ended molecular approach for bacterial identification. Specific aim 2 will investigate if altered microbial profiles in smokers could be attributed to increased severity of disease in this cohort. We will compare the levels of selected organisms between current and never smokers with similar severity of periodontitis. These studies represent the first comprehensive approach to examine the association between smoking and changes in the subgingival microbial community and will provide important preliminary data for much broader research proposals to evaluate the bacterial changes associated with the onset and progression of periodontitis in this high-risk population. The development of a sensitive, high-throughput quantitative assay during the course of this study can be used in the characterization of any microbial ecosystem and will fill a much-needed methodological niche. Identification of putative pathogens and health-associated bacteria in this high-risk population will lead to a better understanding of the role of smoking in the etiology of periodontal diseases. This is an important step in developing clinically useful disease markers and targeted biological interventions. Keywords: periodontitis, smoking, bacteria, subgingival, 16S, molecular microbiology, flow cytometry. These studies represent the first comprehensive approach to examine the association between smoking and changes in the subgingival microbial community. Identification of putative pathogens and health-associated bacteria in this high-risk population will be an important step in studying their interactions with the human host and could lead to a better understanding of the role of smoking in the etiology of periodontal diseases. This could lead to the development of clinically useful disease markers and predictors as well as biological interventions for prevention of disease.